Trouble
by Amelia-Jessica-Pond2012
Summary: When the Doctor, Amy, and Rory decide to go visit River in prison, they run into some trouble. When they come face to face with two of the Doctors worst enemys combined, what will they do? One things leads to another and a battle emerges. Will the Doctor prevail in his battle all will he fail and suffer the losses terribly? Will Silence fall or will the Demons Run?
1. Chapter 1

_Hey Guys!_

_It's my first time writing a fanfic so please bear with me. I love Doctor Who which is why I decided that my first fanfic was going to be a Doctor Who one!_

_I'm listening to Doctor Who music right now (that's how much of a Whovian I am)! Anyways I'm rambling too much so lets skip the conversation and start._

_Allonsy! _

"Umm.. Doctor, why is there a lemon in the bathroom?" a confused Rory asked.

"To ward off the floogles of course! Why else, Rory?" said the Doctor busy twirling around the Tardis, flipping switches and expertly flying the Tardis the way only a 900 year old could do. Amy laughed.

"Doctor!"

"What?" said the Timelord " Everyone knows lemons get rid of floogles!"

"Where are we going this time Doctor? Floogle planet?" said Amy sarcastically.

"What! No that's a silly name! It's Planet Floogle!" replied the Doctor mistaking the exasperated faces of his companions for surprise and wonder.

"And no we're not going there, although that's rather a good idea, the people are very nice and-

"Doctor!"

"Right, sorry I got a bit distracted there. Anyway we're going to StormCage Prison!" He smiled delightedly at the couple.

'We're going to see River?" asked Amy.

"Sure we are!" The familiar grinding noise of the Tardis stopped him. "We're here! Come along Ponds! I'm sure they'll give us a warm welcome!"

He walked to the Tardis doors and flung them open to see a whole army of people pointing guns at the Tardis.

A young man stepped up and said "You're under arrest by the Unified Intelligence Task Force"

"Oh this not good, not good at all." gulped the Doctor.

* * *

That's all for this chapter!

I just love the Ponds don't you? I got so sad when I watched The Angels Take Manhattan.


	2. Chapter 2

_Hey Guys!_

_I'm really shocked and surprised that I already have some followers and reviews! Thanks for the positive feedback guys! Please don't hesitate to give me pointers either because, in my opinion I can always learn more! _

* * *

"Wait did you just say we were under arrest?" asked a confused Rory stumbling out of the Tardis.

"Yes we did. Cuff them." ordered the young officer. 3 men surged up and handcuffed the trio. The officer pushed a button on his earpiece and spoke.

"We've got the captives ma'am, what should we do with them?" There was a brief pause before the officer clicked his earpiece off and nodded to the Doctor and his companions. "You'll need to come with us." He dismissed the rest of his crew before leading the group down a starch white corridor.

"It it just me, or does this place look like a hospital." questioned Amy.

"This place was once a hospital, we just inhabited it." said the officer pushing open a sleek silver door to reveal a waiting room. "Bathrooms that way if you need it." pointed the officer. "You'll be questioned one at a time so you'll need to wait a while." he called over his shoulder while briskly walking away.

"Well Doctor what do we do?" asked Amy confidently. The Doctor started with a confused look on his face.

"Oh Amelia Pond. I don't know." and in that moment he looked old, as old as his age.

"What do you mean? You always know what to do!"

"Listen to me Amy, listen!" he said his gaze burning with intensity. "These people are part of an organization called UNIT, and their ruthless people, they'll do anything to get what they want!"

"Seems like you know a lot about us don't you Doctor? said a malicous voice coming from a black speaker in the corner.

"Yes, I know what you do and how you do it!" yelled the Doctor rising to his feet.

"What a fiesty one. I think we better have you first." A middle aged officer walked in and grabbed the Doctor.

"Madam wants you first. You better come with me." He took the Doctor into a posh sleek office and undid his handcuffs. Then the officer stepped out of the room neatly and closed the door.

"Now you must understand we mean you no harm, Doctor." said a woman sitting in a chair. The Doctor couldn't see her face because the chair was facing the other way, but he thought her voice sounded familiar.

"Who are you?" demanded the Doctor.

"Me? Well I am simply- " she spun around to face the Doctor and looked right in his eyes.

"Madam Kovarian"

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_Cliff-hanger! Keep tuning in for more!_

_3 you guys!_

_Amelia-Jessica-Pond2012_


	3. Chapter 3

_Hi Everyone!_

_I'm so very sorry my chapters are so short but as this is as my first fanfic I thought I might take it easy. But today I'm feeling relaxed so I think I'm ready to try and make a longer chapter!_

_So let the testing commence!_

* * *

"What! But Amy killed you!" the Doctor had a mental flashback of when Amy had confessed she had killed Madam Kovarian.

It had been late at night and he had dropped Amy and Rory back off at their place after a little joy trip in the Tardis. He had said his goodbyes and was just programming the Tardis to leave,when Amy popped her head back in the Tardis looking nervous.

"Doctor? Could I talk to you?" The Doctor had smiled at her and invited her in. She came to stand beside him.

"Back in the other timeline, when you didn't die.."

"Yes Amy?"

"I killed Madam Kovarian. Am I a murderer for that?" The Doctor smiled, she sounded just like Amelia Pond before she grew up.

"It was a parallel timeline, Amy, everything that you did there never existed." With that the Doctor snapped back to reality,"Of course! It was a parallel timeline!"

"Finally caught on have you Doctor? I don't know what everyone's talking about, you're really not that bright are you?" The Doctor flared up.

"I got River on my side!" he retorted.

"Oh that was nothing, just a little trial of whats to come." Madam Kovarian smirked.

"What?"

"Oh this could be entertaining. Why not let have some enjoyment while we take over the world?"

"Wait, what?"

"Oh you sound just like your tenth carnation."

"Wait, how do you know about that, I don't remember you there."

"Oh I've always been there, Doctor, lurking in the shadows. Guards! Turn the cameras in the waiting room on, I want to watch." she ordered.

A guard nodded and marched off.

"Captain Maxley, escort our.. guest to the waiting room, its time to have some fun." she barked maliciously.

"Yes Ma'am" said Captain Maxley with a stiff salute. He led the Doctor back to the waiting room where Amy and Rory where sitting anxiously.

"What's happening? asked Amy immediately.

"You'll find out soon enough, Mrs." replied the Captain before walking away the direction they'd came and locking the door.

"What do we have to do?" said Rory patiently.

"We do what we always do, Rory, figure it out."

** A Few Hours Later**

"We're no closer to figuring it out then we were 3 hours ago!" exclaimed Amy slumped against the hard red seat.

"Are you now!" Everyone jumped, they had forgotten they we're being watched by a camera.

"Well now, we need a bit of motivation don't we? Guards, you know what to do."

Only a few seconds later a pair of strong looking guards came in. "Which one Ma'am? said one in a deep raspy voice.

"Well, I'm feeling nice today, why don't you pick? The guards smiled ferociously.

"Well I say we pick the girl, she doesn't look of any use and she's quite the looker." one smirked. Before anyone could register what was happening the two guards grabbed Amy and pulled her out of the room.

"Amy!" yelled the Doctor and Rory in unison. "Where are you taking her?" roared the Doctor.

"Oh, you'll find out soon enough. For now I suggest you get working or we might have to... help you."

"Doctor what is she doing with Amy?" said the agitated Rory.

"I don't know Rory but we have to keep working this out." He sat down and buried his face in his hands.

"Where are you taking me?" yelled Amy as she struggled against the henchmen's grip. The guards said nothing but marched along a corridor harshly pulling her along with them.

They reached the end of the corridor and turned a corner. They walked on for a few minutes with Amy protesting and wishing that Rory and the Doctor were here with her. They finally reached a door with a brass handle. The guard muttered something into his earpiece before opening the door. They shoved Amy in roughly and slammed the door. Amy heard the metallic _click_ of the lock. Amy looked around taking in her surroundings. The room was bare and dark, holding only a blank tv screen. The tv suddenly flickered, on giving Amy a fright. On the screen a petite blonde woman in a smart blue uniform sat smiling.

"Welcome, the start-up will commence in approximately 10 seconds" she announced.

"Wait, what start-up?" panicked Amy. The woman just smiled and said,  
"Please relax while we begin the countdown."  
"What countdown? What's gonna happen to me?" The woman still smiling irritatingly continued;  
"You'll be put under a light anesthesia while we prepare."  
"Prepare for what?" pressed Amy getting a sinking feeling in her stomach.  
"I'm sorry, you're out of time, the countdown begins." It hit her. She got it now, she knew and now she was scared, terribly, terribly scared, she ran to the door and started banging on it. "Get me out of here!"

"10" the countdown had begun. Amy grabbed the door handle and rattled it only to feel a searing pain in her hand. The handle was burning her! She pulled her hand back with a yelp.

"8"

Amy thought frantically, her mind racing with useless ideas. It was hopeless, she would never get out of here.

"6"

Amy looked up with a jolt. Five already? How had she missed the other numbers?

"5"

She was feeling weak, really weak and longed to just lie down and sleep. No she mustn't, she knew she needed to stay awake.

"4"

She self-consciously she slid to the floor.

"3"

She leaned against the wall wearily.

"2"

She mustered all of her strength to get out those two words before it was too late.

"Help me"

"1"

Her eyes fluttered closed and she fell limp against the wall.

And silence covered the room.

* * *

_Yes I know, very sad and suspense and very crazy towards the end! But don't worry all will be revealed soon! Oh and I will leave you to wonder whether Amy is dead or not._

**_Amelia-Jessica-Pond2012_**


End file.
